There are a number of optical systems in which an object is illuminated with a plurality of light beams which scan the object with light of different wavelengths and polarizations to provide information about the surface of the object. For example, in biological applications, micro-array scanners are used to scan substrates having an array of nucleic acid binding spots on the surface of the substrate after the substrate has been exposed to a solution of interest that contains nucleic acid that is complementary to one or more of the nucleic acid on the substrate. Two or more fluorescent dyes are used to “stain” the spots. The dyes are excited to different degrees depending on the wavelength of light that is directed to the spots. Any given spot may be stained with one, two, or none of the dyes. To measure the quantity of dye at each spot, the spot is illuminated with light that excites the dye and the intensity of light generated by the spot at a predetermined wavelength corresponding to that dye is measured.
To improve the detection efficiency, the intensity of the light emitted from each spot at two different wavelengths when excited by each of the two different excitation wavelengths is measured. In one type of system, the substrate is scanned separately by two different light beams, each light beam having a different wavelength. The intensity of light emitted by the dyes in each spot is measured. The spots on the substrate are on the order of microns and are closely packed; hence, the scanning spots must be on the order of microns.